This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. NAMD (Nanoscale Molecular Dynamics, http://www.ks.uiuc.edu/Research/namd/) is a parallel molecular dynamics code designed for high performance simulation of large biomolecular systems [1, 2]. NAMD employs the prioritized message- driven execution capabilities of the Charm++/Converse parallel runtime system (http://charm.cs.uiuc.edu/), allowing excellent parallel scaling on both massively parallel supercomputers and commodity workstation clusters. NAMD is distributed free of charge to over 37,000 registered users as both source code and convenient precompiled binaries. 8,900 users have downloaded multiple releases. The 2005 NAMD reference paper [47] has been cited over 1000 times. NAMD 2.7b2 was released in November 2009 and has been downloaded by over 4,200 users, 700 of whom are NIH-funded.